Updates to VcfComparator #8973
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Updates to VcfComparator #8973
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gbggrant
approved these changes
Sep 25, 2024
| private boolean ignoreGq0 = false; | ||
|
|
||
| @Argument(fullName = "ignore-multi-allelics", optional = true, doc="Ignore sites where the AC length in the actual matches the actual number of alleles, but doesn't match the expected VC.") | ||
| private boolean ignoreSomeMultiAllelics = false; |
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nit. Should this be ignoreMultiAllelics to be consistent with the fullName (or the other way around?).
| @@ -530,7 +590,7 @@ private void checkAttributes(final Map<String, Object> actual, final Map<String, | |||
| throw makeVariantExceptionFromDifference(key, Double.toString(actualPerAlleleValue), Double.toString(expectedPerAlleleValue)); | |||
| } | |||
| } | |||
| if (key.contains("AS_") && key.contains("RankSum")) { | |||
| if (key.contains("AS_") && key.contains("RankSum") && !key.contains("RAW")) { | |||
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I think
Suggested change
| if (key.contains("AS_") && key.contains("RankSum") && !key.contains("RAW")) { | |
| if (key.startsWith("AS_") && key.contains("RankSum") && !key.contains("RAW")) { |
is a little more correct?
| @@ -546,11 +606,25 @@ private void checkAttributes(final Map<String, Object> actual, final Map<String, | |||
| logger.warn("GATK version-specific NaN versus empty AS_RAW annotation discrepancy"); | |||
| } | |||
| } | |||
| } else if (key.contains("AS_") && key.contains("RAW") && key.contains("RankSum")) { | |||
| if (((String) actualList.get(i)).isEmpty() && ((String) expectedList.get(i)).isEmpty()) { | |||
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Same comment about using startsWith here.
| @@ -515,7 +568,14 @@ private void checkAttributes(final Map<String, Object> actual, final Map<String, | |||
| } | |||
| } | |||
| //we've already gotten rid of stars... I think -- do we have to sort the alts? Maybe... I should be using my own AlleleSpecificAnnotationData!!! | |||
| final int iterationEnd = ignoreNonRefData && actualAlts.contains(Allele.NON_REF_ALLELE) ? expectedAlts.size()-1 : expectedAlts.size(); //exclusive | |||
| int iterationEnd = ignoreNonRefData && actualAlts.contains(Allele.NON_REF_ALLELE) ? expectedAlts.size()-1 : expectedAlts.size(); //exclusive | |||
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Could keep the final here by doing something like:
final iterationEnd = if (key.equals(...) {
3
} else if (key.equals(...) {
5
} else {
...
}
| if (key.equals(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY)) { | ||
| iterationEnd = 3; | ||
| } | ||
| if (key.equals(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY)) { |
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These changes add arguments specific to the update from GATK 4.5.0.0 -> 4.6.0.0 that special case sites that were flagged previously in the WARP tests. Most of the sites that can now be skipped are based on the no call changes that were expected with this update to JointCalling and ReblockGVCFs. There are also some small changes to HaplotypeCaller at low quality sites that are then dropped by ReblockGVCFs.
Additionally there were some expected changes to the Ultima pipelines in HaplotypeCaller and JointCalling which can now be skipped by the VcfComparator tool.
Finally if AD is 0 for non-ref reads (which can happen with DRAGEN input), then AS_QD has jitter added which is now accounted for.